# [gmx-users] HREX simulation

Shyno Mathew sm3334 at columbia.edu
Mon Aug 31 16:57:38 CEST 2015

```Dear Prof. Shirts, Prof. Abraham,

Thanks so much for the detailed explanation. Sorry for the delay in
responding, I didn't see the replies till now!
I did increase the number of replicas, hope to see better results.

have a great day,
Shyno

On Thu, Aug 27, 2015 at 12:35 PM, Shyno Mathew <sm3334 at columbia.edu> wrote:

> Dear all,
>
> I am new to doing replica exchange simulations.
> I am trying to understand the empirical transition matrix printed in the
> log files. I tried exchange intervals 2 ps and 0.2 ps. However, later I
> read gromacs recommends exchange interval not to be under 1ps. The system
> is protein in water and I am only showing parts of the matrix:
>
> Exchange interval: 0.2 ps
> Repl            1            2            3            4             5
>
> Repl  0.9528  0.0472  0.0000  0.0000  0.0000
> Repl  0.0472  0.9017  0.0511  0.0000  0.0000
> Repl  0.0000  0.0511  0.8946  0.0543  0.0000
> Repl  0.0000  0.0000  0.0543  0.8898  0.0558
>
> 1. If I look at line 3 ""Repl  0.0472  0.9017  0.0511" does this mean
> exchange between replica 1, 2 is accepted 4.72 %  and exchange between 2,3
> is accepted 5.11 % ?
>
> Repl            1            2            3            4             5
>
>
> Repl  0.9504  0.0496   0.0000  0.0000  0.0000
>
> Repl  0.0496  0.8982  0.0522   0.0000  0.0000
>
> Repl  0.0000  0.0522  0.8942  0.0536   0.0000
>
> Repl  0.0000  0.0000  0.0536  0.8888  0.0576
>
> 2. With exchange interval 2 ps, I am getting slightly better acceptance
> rate. For example, again looking at line 3 "Repl  0.0496  0.8982  0.0522"
> the acceptance rate for exchange 1 to 2 is 4.96 %, and he acceptance rate
> for exchange 2 to 3 is 5.22 %
>
> thanks,
> Shyno
>
>
> --
> Shyno Mathew
> PhD Candidate
> Department of Chemical Engineering
> Office of Graduate Student Affairs
> The Fu Foundation School Of Engineering and Applied Science
> Columbia University
>

--
Shyno Mathew
PhD Candidate
Department of Chemical Engineering